A whole-slide foundation model for digital pathology from real-world data.

Digital pathology poses unique computational challenges, as a standard gigapixel slide may comprise tens of thousands of image tiles1-3. Prior models have often resorted to subsampling a small portion of tiles for each slide, thus missing the important slide-level context4. Here we present Prov-GigaPath, a whole-slide pathology foundation model pretrained on 1.3 billion 256 × 256 pathology image tiles in 171,189 whole slides from Providence, a large US health network comprising 28 cancer centres. The slides originated from more than 30,000 patients covering 31 major tissue types. To pretrain Prov-GigaPath, we propose GigaPath, a novel vision transformer architecture for pretraining gigapixel pathology slides. To scale GigaPath for slide-level learning with tens of thousands of image tiles, GigaPath adapts the newly developed LongNet5 method to digital pathology. To evaluate Prov-GigaPath, we construct a digital pathology benchmark comprising 9 cancer subtyping tasks and 17 pathomics tasks, using both Providence and TCGA data6. With large-scale pretraining and ultra-large-context modelling, Prov-GigaPath attains state-of-the-art performance on 25 out of 26 tasks, with significant improvement over the second-best method on 18 tasks. We further demonstrate the potential of Prov-GigaPath on vision-language pretraining for pathology7,8 by incorporating the pathology reports. In sum, Prov-GigaPath is an open-weight foundation model that achieves state-of-the-art performance on various digital pathology tasks, demonstrating the importance of real-world data and whole-slide modelling.

Comparative vaccine effectiveness against severe COVID-19 over time in US hospital administrative data: a case-control study.

BACKGROUND: Research suggests the protection offered by COVID-19 vaccines might wane over time, prompting consideration of booster vaccinations. Data on which vaccines offer the most robust protection over time, and which patients are most vulnerable to attenuating protection, could help inform potential booster programmes. In this study, we used comprehensive hospitalisation data to estimate vaccine effectiveness over time. METHODS: In this case-control study, we used data from a large US health-care system to estimate vaccine effectiveness against severe SARS-CoV-2 infection and examined variation based on time since vaccination, vaccine type, and patients' demographic and clinical characteristics. We compared trends in attenuation of protection across vaccines and used a multivariable model to identify key factors associated with risk for severe breakthrough infection. Patients were considered to have severe COVID-19 if they were admitted to the hospital, had a final coded diagnosis of COVID-19 (according to International Classification of Diseases Tenth Revision code U07.1) or a positive nucleic acid amplification test for symptomatic SARS-CoV-2 during their hospitalisation, and were treated with remdesivir or dexamethasone during hospitalisation. FINDINGS: Between April 1, 2021, and Oct 26, 2021, we observed 9667 admissions for severe COVID-19 (ie, cases). Overall, 1293 (13·4%) of 9667 cases were fully vaccinated at the time of admission, compared with 22 308 (57·7%) of 38 668 controls, who were admitted to hospital for other reasons. The median time between vaccination and hospital admission among cases was 162 days (IQR 118-198). Overall vaccine effectiveness declined mostly over the course of the summer, from 94·5% (95% CI 91·4-96·5) in April, 2021 (pre-delta), to 84·0% (81·6-86·1) by October, 2021. Notably, vaccine effectiveness declined over time, from 94·0% (95% CI 92·8-95·0) at days 50-100 after vaccination to 80·4% (77·8-82·7) by days 200-250 after vaccination. After 250 days, vaccine effectiveness declines were even more notable. Among those who received the BNT162b2 (Pfizer-BioNTech) vaccine, vaccine effectiveness fell from an initial peak of 94·9% (93·2-96·2) to 74·1% (69·6-77·9) by days 200-250 after vaccination. Protection from the mRNA-1273 (Moderna) and Ad26.COV2 (Janssen) vaccines declined less over time, although the latter offered lower overall protection. Holding other factors constant, the risk of severe breakthrough infection was most strongly associated with age older than 80 years (adjusted odds ratio 1·76, 95% CI 1·43-2·15), vaccine type (Pfizer 1·39, 0·98-1·97; Janssen 14·53, 8·43-25·03; both relative to Moderna), time since vaccination (1·05, 1·03-1·07; per week after week 8 when protection peaks, technically), and comorbidities including organ transplantation (3·44, 95% CI 2·12-5·57), cancer (1·93, 1·60-2·33), and immunodeficiency (1·49, 1·13-1·96). INTERPRETATION: Vaccination remains highly effective against hospitalisation, but vaccine effectiveness declined after 200 days, particularly for older patients or those with specific comorbidities. Additional protection (eg, a booster vaccination) might be warranted for everyone, but especially for these populations. In addition to promoting general vaccine uptake, clinicians and policy makers should consider prioritising booster vaccinations in those most at risk of severe COVID-19. FUNDING: None.

Remdesivir and Mortality in Patients With Coronavirus Disease 2019.

BACKGROUND: The impact of remdesivir (RDV) on mortality rates in coronavirus disease 2019 (COVID-19) is controversial, and the mortality effect in subgroups of baseline disease severity has been incompletely explored. The purpose of this study was to assess the association of RDV with mortality rates in patients with COVID-19. METHODS: In this retrospective cohort study we compared persons receiving RDV with those receiving best supportive care (BSC). Patients hospitalized between 28 February and 28 May 2020 with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection were included with the development of COVID-19 pneumonia on chest radiography and hypoxia requiring supplemental oxygen or oxygen saturation ≤94% with room air. The primary outcome was overall survival, assessed with time-dependent Cox proportional hazards regression and multivariable adjustment, including calendar time, baseline patient characteristics, corticosteroid use, and random effects for hospital. RESULTS: A total of 1138 patients were enrolled, including 286 who received RDV and 852 treated with BSC, 400 of whom received hydroxychloroquine. Corticosteroids were used in 20.4% of the cohort (12.6% in RDV and 23% in BSC). Comparing persons receiving RDV with those receiving BSC, the hazard ratio (95% confidence interval) for death was 0.46 (.31-.69) in the univariate model (P < .001) and 0.60 (.40-.90) in the risk-adjusted model (P = .01). In the subgroup of persons with baseline use of low-flow oxygen, the hazard ratio (95% confidence interval) for death in RDV compared with BSC was 0.63 (.39-1.00; P = .049). CONCLUSION: Treatment with RDV was associated with lower mortality rates than BSC. These findings remain the same in the subgroup with baseline use of low-flow oxygen.

Nonimpact of Decolonization as an Adjunctive Measure to Contact Precautions for the Control of Methicillin-Resistant Staphylococcus aureus Transmission in Acute Care.

This was an observational study comparing methicillin-resistant Staphylococcus aureus (MRSA) transmission with no decolonization of medical patients to required decolonization of all MRSA carriers during two consecutive periods: baseline with no decolonization of medical patients (16 months) and universal MRSA carrier decolonization (13 months). The setting was a one-hospital, 156-bed facility with 9,200 annual admissions. Regression models were used to compare rates of MRSA acquisition. The chi-square test was used to compare event frequencies. We used rates of MRSA clinical disease as an outcome monitor of the program. Analysis was done on 15,666 patients who had admission and discharge tests; 27.9% of inpatient days were occupied by a MRSA-positive patient (colonized patient-days) who received decolonization while hospitalized during the baseline period (this 27.9% represented those who had planned surgery) compared to 76.0% during the intervention period (P < 0.0001). The rate of MRSA transmission was 97 events (1.0%) for 9,415 admissions (2.0 transmission events/1,000 patient-days) during baseline and was 87 (1.4%) for 6,251 admissions (2.7 transmission events/1,000 patient-days) during intervention (P = 0.06; rate ratio, 0.74; 95% confidence interval [CI], 0.55 to 1.00). The MRSA nosocomial clinical disease rate was 5.9 infections/10,000 patient-days in the baseline period and was 7.2 infections/10,000 patient-days for the intervention period (rate ratio, 0.82; 95% CI, 0.46 to 1.45; P = 0.49). Decolonization of MRSA patients does not add benefit when contact precautions are used for patients colonized with MRSA in acute (hospital) care.

Severe Influenza in 33 US Hospitals, 2013-2014: Complications and Risk Factors for Death in 507 Patients.

BACKGROUND: Influenza A (H1N1) pdm09 became the predominant circulating strain in the United States during the 2013-2014 influenza season. Little is known about the epidemiology of severe influenza during this season. METHODS: A retrospective cohort study of severely ill patients with influenza infection in intensive care units in 33 US hospitals from September 1, 2013, through April 1, 2014, was conducted to determine risk factors for mortality present on intensive care unit admission and to describe patient characteristics, spectrum of disease, management, and outcomes. RESULTS: A total of 444 adults and 63 children were admitted to an intensive care unit in a study hospital; 93 adults (20.9%) and 4 children (6.3%) died. By logistic regression analysis, the following factors were significantly associated with mortality among adult patients: older age (>65 years, odds ratio, 3.1 [95% CI, 1.4-6.9], P=.006 and 50-64 years, 2.5 [1.3-4.9], P=.007; reference age 18-49 years), male sex (1.9 [1.1-3.3], P=.031), history of malignant tumor with chemotherapy administered within the prior 6 months (12.1 [3.9-37.0], P<.001), and a higher Sequential Organ Failure Assessment score (for each increase by 1 in score, 1.3 [1.2-1.4], P<.001). CONCLUSION: Risk factors for death among US patients with severe influenza during the 2013-2014 season, when influenza A (H1N1) pdm09 was the predominant circulating strain type, shifted in the first postpandemic season in which it predominated toward those of a more typical epidemic influenza season.

Outpatient advance care planning for patients with metastatic cancer: a pilot quality improvement initiative.

BACKGROUND: Despite American Society of Clinical Oncology (ASCO) and National Comprehensive Cancer Network (NCCN) guidelines recommending that oncologists discuss advance care planning (ACP) with patients with stage IV cancer early in treatment, in standard practice ACP remains a late step of a terminal illness. ACP preserves comfort and dignity at the end of life, ensuring patients receive the care that they desire. METHODS AND MATERIALS: A feasibility study in patients with stage IV cancer was developed to test whether incorporating ACP immediately after a stage IV cancer diagnosis is feasible. Inclusion criteria were consecutive new gastrointestinal and thoracic oncology patients treated by one of two oncologists. The project included creation of new workflow; development of an ACP patient education guidebook; training seminars for oncology staff; and enhancements to the electronic health record (EHR) to improve ACP documentation. RESULTS: The oncologists recorded 33 of 48 (69%) advance directive notes (ADNs) and 22 of 48 (46%) code status orders (CSOs) in the EHR of patients newly diagnosed with stage IV cancer by following ACP protocol during the 6-month trial period. Twenty-one of 33 ADNs were entered within 7 days of first consultation. The median time to ADN placement was 1 day after consultation. Twenty-two of 33 patients with ADNs had CSOs placed, of which 16 were do-not-resuscitate (DNR) and 6 were full code. One year prior to the feasibility study, only 1 of 75 deceased patients of the two oncologists had outpatient ADNs and CSOs. CONCLUSIONS: Outpatient ACP is feasible early in the care of patients with stage IV cancer through systematic improvement in workflow and motivated providers. Education and infrastructure were pivotal to routine development of advance care plans.

Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli.

BACKGROUND: Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins--potentially critical for control efforts--remain undefined. METHODS: Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967-2009) E. coli isolates representing sequence type ST131 and 853 recent (2010-2011) consecutive E. coli isolates from 5 clinical laboratories in Seattle, Washington, and Minneapolis, Minnesota. Clonal structure was resolved based on fimH sequence (fimbrial adhesin gene: H subclone assignments), multilocus sequence typing, gyrA and parC sequence (fluoroquinolone resistance-determining loci), and pulsed-field gel electrophoresis. RESULTS: Of the recent fluoroquinolone-resistant clinical isolates, 52% represented a single ST131 subclonal lineage, H30, which expanded abruptly after 2000. This subclone had a unique and conserved gyrA/parC allele combination, supporting its tight clonality. Unlike other ST131 subclones, H30 was significantly associated with fluoroquinolone resistance and was the most prevalent subclone among current E. coli clinical isolates, overall (10.4%) and within every resistance category (11%-52%). CONCLUSIONS: Most current fluoroquinolone-resistant E. coli clinical isolates, and the largest share of multidrug-resistant isolates, represent a highly clonal subgroup that likely originated from a single rapidly expanded and disseminated ST131 strain. Focused attention to this strain will be required to control the fluoroquinolone and multidrug-resistant E. coli epidemic.

Epidemiology of methicillin-resistant Staphylococcus aureus carriage and MRSA surgical site infections in patients undergoing colorectal surgery: a cohort study in two centers.

BACKGROUND: Surgical site infections (SSIs) after colorectal surgery usually are caused by commensal intestinal bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) may be responsible for additional SSI-related morbidity. The aim of this retrospective cohort study was to describe the epidemiology of SSIs caused by MRSA after colorectal surgery in two tertiary-care centers, one in Geneva, Switzerland (G), and the other in Chicago, Illinois (C). METHODS: Adult patients undergoing colorectal resections during periods of universal screening for MRSA on admission were identified retrospectively. Demographic characteristics, surgery-related factors, and occurrence of MRSA SSI were compared in patients with and without MRSA carriage before surgery. RESULTS: There were 1,069 patients (G=194, C=875) with a median age of 67 years fulfilling the inclusion criteria. Of these, 45 patients (4.2%) had a positive MRSA screening result within 30 days before surgery (G=18, C=27; p<0.001). Ten patients (0.9%; G=6, C=4) developed MRSA SSI, detected a median of 17.5 days after surgery, but only two of them were MRSA-positive before surgery. Nine of the 45 MRSA carriers identified by screening received pre-operative prophylaxis with vancomycin (G 6/18, C 3/27), and 17 of these patients (37.8%; G 7/18, C 10/27) were started on MRSA decolonization therapy before surgery. Pre-operative administration of either decolonization or vancomycin was not protective against MRSA SSI (p=0.49). CONCLUSION: Methicillin-resistant S. aureus seems to be an infrequent cause of SSI after colorectal resections, even in MRSA carriers. Systematic universal screening for MRSA carriage prior to colorectal surgery may not be beneficial for the individual patient. Post-operative factors seem to be important in MRSA infections, as the majority of MRSA SSIs occurred in patients negative for MRSA carriage.

Laboratory testing for Clostridium difficile infection: light at the end of the tunnel.

Clostridium difficile infection (CDI) is changing as evidenced by increasing virulence, rising incidence, unresponsiveness to metronidazole therapy, and worse outcomes. Thus, it is critical that CDI diagnosis be accurate so ongoing epidemiology, disease prevention, and treatment remain satisfactory. We tested 10 diagnostic assays, including 1 commercial real-time polymerase chain reaction (qPCR) test for the laboratory detection of toxigenic C difficile on 1,000 stool samples. Sensitive culture for toxigenic C difficile using 2 types of media with broth enrichment defined the reference standard. For the study, 1,000 tests were performed on samples from 919 patients. Of the samples, 146 contained evidence for toxigenic C difficile and represented the true-positive results. Only the US Food and Drug Administration-cleared qPCR assay (Becton Dickinson, Franklin Lakes, NJ) and 1 glutamate dehydrogenase test (TechLab, Blacksburg, VA) were not statistically inferior to culture in sensitivity. The common enzyme immunoassay tests all had sensitivity values less than 50%. Clinical laboratory professionals need to seriously consider their diagnostic testing and use the assays that perform best for the detection of CDI.

Decolonization therapy in infection control.

PURPOSE OF REVIEW: Hospital acquired infections (HAIs) are costly and are a leading cause of hospital death. Many HAIs originate from patients' own flora. Decolonization strategies aim to prevent infection from these endogenous sources. This review focuses on data published from 2008 to the present on effectiveness and safety of patient decolonization strategies for preventing HAIs. RECENT FINDINGS: Surgical site infections (SSIs): recent literature confirms that Staphylococcus aureus decolonization to prevent SSIs is effective in cardiac and likely certain orthopedic surgery patients. The benefit to general surgery patients is not clear. Ventilator-associated pneumonia (VAP): although past studies have found that decolonization benefits cardiac surgery patients, recent studies have not found the same benefit in general medical and surgical ICU patients. Blood stream infection (BSI): mupirocin on hemodialysis catheter exit sites is protective against BSI. Chlorhexidine and selective decontamination of the digestive tract have been studied as ways to decrease ICU BSI, but their roles are still being clarified. Methicillin-resistant Staphylococcus aureus (MRSA)-specific decolonization: evidence of benefit to MRSA-colonized nonsurgical patients is lacking. SUMMARY: Decolonization is likely an effective infection-control strategy for hemodialysis catheter-associated infections and in cardiac and orthopedic surgery patients. More research is needed on its role in other settings.

Does my patient have Clostridium difficile infection?

Clostridium difficile infection (CDI) seems to be changing-with increasing virulence and incidence, more resistance to metronidazole, and worse outcomes. Accurate diagnosis is critical, but 3 common misconceptions lead to misdiagnosis: Clostridium difficile infection is a possibility when the patient has fewer than 3 loose stools per day; the glutamate dehydrogenase test for CDI is sensitive and thus is a good initial test; and repeating an insensitive laboratory test for CDI is useful. These misconceptions can lead to missed diagnoses (for example, when tests with low sensitivity are used) and to false diagnoses (for example, when tests are done in patients who are unlikely to have CDI because they have minimal diarrhea or negative results on recent tests). Diagnoses of CDI will be more accurate if clinicians use tests with a higher sensitivity, reduce the frequency of testing for a single episode of diarrhea, and give more attention to key elements of the patient's history.